I think she's saying that she got it wrong from the beginning. Once that's happened then the characters are steered together by the plot and so of course it looks natural. I think Harry and Hermione would have been very happy together, but for all that I like that Harry and Ginny got together. It doesn't seem to come across quite so well in the films, the suspicion being that either Bonnie Wright isn't all that good an actor or that the filmmakers didn't spend enough time focusing on that couple, but in the books I think it's the right relationship for Harry.
Don't think it's all that big a deal one way or the other, but once you decide that the book is going to end with various romances that last it's difficult to see how else things could be paired off given the lack of central teenage girls in the book outside Hermione, Ginny and Luna (who ends up, rightly, with Neville if memory serves). So what other pairing is there but Harry/ Ginny and Ron/ Hermione?